Secondary structure and small RNA-seq evidence for dme-mir-4914

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:2737553-2737676 + AGACGAGCCCACAACGTGAGTGA-GAGCGAGT------TCCAAT-----------------------GTGGTCC----------------------TCGAAACCAGTTGTGCTTCGATCAGATTCCAAAATTGACACATT--CCG---------------------------------ACCTTGAATCA-CCCACAGCGGATTGGACAGCTC
droSim1 chr2L:2697912-2698035 + AGACGAGCCCACAACGTGAGTGA-GAGCGAGT------TTCATT-----------------------GTGGTCC----------------------TCGAAACCAGTTGCGCTCCGATCAGATTCCAAAATTGACACATT--CCG---------------------------------ACCTTGAATCA-CCCACAGCGGCTTGGACAGCTC
droSec1 super_5:903635-903758 + AGACGAGCCCACAACGTGAGTGA-GAGCGAGT------TCCATT-----------------------GTGGTCC----------------------TCGAAACCAGTTGCGCTCCGATCAGATTCCAAAATTGACACATT--CCG---------------------------------ACCTTGAATCA-CCCACAGCGGCTTGGACAGCTC
droYak2 chr2L:2732711-2732833 + AGACGAGCCCACAACGTGAGTGA-GA----------GGTCCATT-----G-----------T-----GTGATCC----------------------CCAAAACCAGTTCTACTCAGATCTGATTCC-AAATTGACACATTCTCTG---------------------------------ACCTTGAATCA-CCCACAGCGGATTGGATAGCTC
droEre2 scaffold_4929:2790150-2790269 + AGACGAGCCCACAACGTGAGTGA-GA----------GGTCCATT-----------------------GTGGTCC----------------------TTGAAACCAGTTCCGCTCGGTTCATGATGCCAGATTGACACATT--CCG---------------------------------ACCTTTAATCA-CCCACAGCGGATTGGACAGCTC
droAna3 scaffold_12916:13439490-13439581 + GGACGAGCCAACAACGTAAGT--------------------------------------------------TCT----------------------CTGAAACCATTC----------CAATTTTCAAACTTATCAAGTT--G-----------------------------------TTAATGTCTTT-CACACAGGGGCTTGGATAGTTC
dp4 chr4_group4:2073904-2074060 + AGACGAGCCCACAACGTAAGTATCGAACGAGTGAGAGGACCA-GACCAG--AGGCAGCATCTGCGATGCGGTCGAAAAGAGAAGAGAAACCAGAGAGCTAAACCAGTTGCTGACT-----------------GACATTCC--ACA---------------------------------ACCTTGAACCATCCCACAGAGGCCTGGATAGTTC
droPer1 super_10:1078988-1079144 + AGACGAGCCCACAACGTAAGTATCGAACGAGTGAGAGGACCA-GACCAG--AGGCAGCATCTGCGATGCGGTCGAAAAGAGAAGAGAAACCAGAGAGCTAAACCAGTTGCTGACT-----------------GACATTCC--ACA---------------------------------ACCTTGAACCATCCCACAGAGGCCTGGATAGTTC
droWil1 scaffold_180772:1508923-1509021 + AGACGAGCCCACAACGTAAGTAA-TAACAAA------------------------------------------------------------------AAAGACCGGTTATTTCCT-----------------G---------TTAGCCTTGAACTTAACCAACATCTC-------------------AA-CCAACAGAGGCCTGGACAGCTC
droVir3 scaffold_12963:11356884-11356997 + AGACGAGCCCACAACGTAAGCAA-GAATAGAG------A------ATGCAATCAAT-----------G----------------------------CGGAAACCAGTTGCTGACT-----------------AACATGTG--CTTACCTTGAAATTG-----T---------------------AACCA-TTCGCAGGGGCCTGGATAGTTC
droMoj3 scaffold_6308:1548466-1548588 - CGACGAGCCCACGTCGGGCCTGG-------A-----C-TCCTTTACCGC--CCACAGC---------------------------------------GTC---------------GTCCAGGTGCTGAAGAAGCTA----------TCGCAAAAGGG-----CAAGACCGTCATACTGACCATACATCA-GCCATCG----TCGGAGCTCTT
droGri2 scaffold_15252:5474360-5474483 + GGACGAGCCCACAACGTAAGTGA-AA----------CA-CCGAAACACCA-----------C-----ACAATC------------------------GAGAACCAGTTACTGACT----AA------GCATTATTATTTT--TTAACCTTGAAATTG-----CATCGC------------------ATC-CATACAGGGGCCTGGACAGTTC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:2737553-2737676 + AGACGAGCCCACAACGTGAGTGAGAGCGAGTTCCAATG--TGGTCCTCGAAACCAGTTGTGCTTCGATCAGATTCCAAAATTGACACATTC--CGACCTTGAATCACCCACAGCGGATTGGACAGCTC
droSim1 chr2L:2697912-2698035 + AGACGAGCCCACAACGTGAGTGAGAGCGAGTTTCATTG--TGGTCCTCGAAACCAGTTGCGCTCCGATCAGATTCCAAAATTGACACATTC--CGACCTTGAATCACCCACAGCGGCTTGGACAGCTC
droSec1 super_5:903635-903758 + AGACGAGCCCACAACGTGAGTGAGAGCGAGTTCCATTG--TGGTCCTCGAAACCAGTTGCGCTCCGATCAGATTCCAAAATTGACACATTC--CGACCTTGAATCACCCACAGCGGCTTGGACAGCTC
droYak2 chr2L:2732711-2732833 + AGACGAGCCCACAACGTGAGTGAGA----GGTCCATTGTGTGATCCCCAAAACCAGTTCTACTCAGATCTGATTCCA-AATTGACACATTCTCTGACCTTGAATCACCCACAGCGGATTGGATAGCTC
droEre2 scaffold_4929:2790150-2790269 + AGACGAGCCCACAACGTGAGTGAGA----GGTCCATTG--TGGTCCTTGAAACCAGTTCCGCTCGGTTCATGATGCCAGATTGACACATTC--CGACCTTTAATCACCCACAGCGGATTGGACAGCTC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AGACGAGCCCACAACGTGAGTGA-GAGCGAGT--------------------------TTCATTGTGGTCC----------------------TCGAAACCAGTTGCGCTCCGATCAGATTCCAAAATTGACACATTCCGACCTTGAATCA-CCCACAGCGGCTTGGACAGCTCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AGACGAGCCCACAACGTAAGTATCGAACGAGTGAGAGGACCAGACCAGAGGCAGCATCTGCGATGCGGTCGAAAAGAGAAGAGAAACCAGAGAGCTAAACCAGTTGCTG-----------------ACTGACATTCCACAACCTTGAACCATCCCACAGAGGCCTGGATAGTTCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-19.0,  p-value=0.009901 dG=-18.3,  p-value=0.009901

droSim1

dG=-15.0,  p-value=0.009901 dG=-15.0,  p-value=0.009901 dG=-14.9,  p-value=0.009901 dG=-14.9,  p-value=0.009901 dG=-14.9,  p-value=0.009901 dG=-13.1,  p-value=0.009901

droSec1

dG=-15.7,  p-value=0.009901 dG=-15.7,  p-value=0.009901 dG=-15.3,  p-value=0.009901 dG=-15.3,  p-value=0.009901 dG=-15.2,  p-value=0.009901 dG=-14.2,  p-value=0.009901

droYak2

dG=-22.7,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-22.1,  p-value=0.009901

droEre2

dG=-22.9,  p-value=0.009901 dG=-22.9,  p-value=0.009901 dG=-22.9,  p-value=0.009901 dG=-22.8,  p-value=0.009901 dG=-22.8,  p-value=0.009901

droAna3

dG=-4.6,  p-value=0.009901 dG=-3.9,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.7,  p-value=0.009901 dG=-3.6,  p-value=0.009901

dp4

dG=-20.5,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.2,  p-value=0.009901

droPer1

dG=-20.5,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.2,  p-value=0.009901

droWil1

dG=-3.9,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.5,  p-value=0.009901 dG=-3.5,  p-value=0.009901 dG=-3.3,  p-value=0.009901

droVir3

dG=-11.0,  p-value=0.009901 dG=-10.8,  p-value=0.009901 dG=-10.6,  p-value=0.009901 dG=-10.4,  p-value=0.009901 dG=-10.3,  p-value=0.009901

droMoj3

dG=-23.1,  p-value=0.009901 dG=-22.7,  p-value=0.009901

droGri2

dG=-4.3,  p-value=0.009901 dG=-4.2,  p-value=0.009901 dG=-3.7,  p-value=0.009901 dG=-3.5,  p-value=0.009901 dG=-3.4,  p-value=0.009901 dG=-3.1,  p-value=0.009901

Generated: 03/07/2013 at 05:34 PM